{"id":"https://openalex.org/W1979258327","doi":"https://doi.org/10.1186/1748-7188-3-10","title":"A stitch in time: Efficient computation of genomic DNA melting bubbles","display_name":"A stitch in time: Efficient computation of genomic DNA melting bubbles","publication_year":2008,"publication_date":"2008-07-17","ids":{"openalex":"https://openalex.org/W1979258327","doi":"https://doi.org/10.1186/1748-7188-3-10","mag":"1979258327","pmid":"https://pubmed.ncbi.nlm.nih.gov/18637171"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-3-10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-3-10","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-3-10","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-3-10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Eivind T\u00f8stesen","orcid":null},"institutions":[{"id":"https://openalex.org/I2801049993","display_name":"Norwegian Cancer Society","ror":"https://ror.org/01925vb10","country_code":"NO","type":"nonprofit","lineage":["https://openalex.org/I2801049993"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Eivind T\u00f8stesen","raw_affiliation_strings":["Department of Tumor Biology, Norwegian Radium Hospital, N-0310, Oslo, Norway. eivindto@math.uio.no"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Tumor Biology, Norwegian Radium Hospital, N-0310, Oslo, Norway. eivindto@math.uio.no","institution_ids":["https://openalex.org/I2801049993"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I2801049993"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.4207,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.63025597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"3","issue":"1","first_page":"10","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.2500999867916107,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.2500999867916107,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.147599995136261,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.14259999990463257,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.7167999744415283},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4932999908924103},{"id":"https://openalex.org/keywords/genomic-dna","display_name":"genomic DNA","score":0.47530001401901245},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4713999927043915},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.39730000495910645},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.37540000677108765}],"concepts":[{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.7167999744415283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6190999746322632},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5389000177383423},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4932999908924103},{"id":"https://openalex.org/C17757408","wikidata":"https://www.wikidata.org/wiki/Q4135516","display_name":"genomic DNA","level":3,"score":0.47530001401901245},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4713999927043915},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.39730000495910645},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.37540000677108765},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.374099999666214},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3691999912261963},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35569998621940613},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3296999931335449},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3255000114440918},{"id":"https://openalex.org/C3018263672","wikidata":"https://www.wikidata.org/wiki/Q1296251","display_name":"Efficient algorithm","level":2,"score":0.3000999987125397},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.2727000117301941},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2685000002384186},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.2662000060081482}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/1748-7188-3-10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-3-10","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-3-10","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:18637171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18637171","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:arXiv.org:0802.1057","is_oa":true,"landing_page_url":"http://arxiv.org/abs/0802.1057","pdf_url":"https://arxiv.org/pdf/0802.1057","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:4126e9d603ea410aa0ae270b570c9280","is_oa":false,"landing_page_url":"https://doaj.org/article/4126e9d603ea410aa0ae270b570c9280","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 3, Iss 1, p 10 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2553405","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2553405","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"},{"id":"pmh:oai:www.duo.uio.no:10852/46518","is_oa":true,"landing_page_url":"http://hdl.handle.net/10852/46518","pdf_url":null,"source":{"id":"https://openalex.org/S4306401716","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-3-10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-3-10","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-3-10","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1979258327.pdf","grobid_xml":"https://content.openalex.org/works/W1979258327.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1566214213","https://openalex.org/W1964379758","https://openalex.org/W1965118572","https://openalex.org/W1976016360","https://openalex.org/W1981135687","https://openalex.org/W1987854744","https://openalex.org/W1989162094","https://openalex.org/W1989215959","https://openalex.org/W1993477247","https://openalex.org/W1996259602","https://openalex.org/W2001307989","https://openalex.org/W2005738732","https://openalex.org/W2014095962","https://openalex.org/W2017147864","https://openalex.org/W2017407107","https://openalex.org/W2021356303","https://openalex.org/W2022375607","https://openalex.org/W2022916085","https://openalex.org/W2025956225","https://openalex.org/W2034013107","https://openalex.org/W2042282283","https://openalex.org/W2048046856","https://openalex.org/W2048855496","https://openalex.org/W2054115419","https://openalex.org/W2057703537","https://openalex.org/W2074662966","https://openalex.org/W2074718407","https://openalex.org/W2074949379","https://openalex.org/W2088306370","https://openalex.org/W2088922607","https://openalex.org/W2093860423","https://openalex.org/W2097632362","https://openalex.org/W2105122253","https://openalex.org/W2119447107","https://openalex.org/W2119699021","https://openalex.org/W2123766602","https://openalex.org/W2142072523","https://openalex.org/W2168393276","https://openalex.org/W2320627770","https://openalex.org/W3122583070","https://openalex.org/W3123295715"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"It":[1],"is":[2,38,44,55,105,145],"of":[3,10,13,33,52,74,110,128,141,149,166],"biological":[4],"interest":[5],"to":[6,87],"make":[7],"genome-wide":[8,164],"predictions":[9],"the":[11,24,49,53,89,96,98,129,133,163],"locations":[12],"DNA":[14],"melting":[15],"bubbles":[16,111,167],"using":[17],"statistical":[18],"mechanics":[19],"models.":[20],"Computationally,":[21],"this":[22],"poses":[23],"challenge":[25],"that":[26,48,63],"a":[27,71,75,101,106,118,125],"generic":[28],"search":[29],"through":[30],"all":[31],"combinations":[32],"bubble":[34,64,77],"starts":[35],"and":[36,112,138,174],"ends":[37],"quadratic.":[39,59],"RESULTS:":[40],"An":[41],"efficient":[42],"algorithm":[43,61,99,116],"described,":[45],"which":[46,104],"shows":[47],"time":[50,90],"complexity":[51],"task":[54],"O(NlogN)":[56],"rather":[57],"than":[58,93],"The":[60,115],"exploits":[62],"lengths":[65],"may":[66],"be":[67],"limited,":[68],"but":[69],"without":[70],"prior":[72],"assumption":[73],"maximal":[76],"length.":[78],"No":[79],"approximations,":[80],"such":[81],"as":[82],"windowing,":[83],"have":[84,152],"been":[85,153],"introduced":[86],"reduce":[88],"complexity.":[91],"More":[92],"just":[94],"finding":[95,121],"bubbles,":[97],"produces":[100],"stitch":[102,143],"profile,":[103],"probabilistic":[107],"graphical":[108],"model":[109],"helical":[113],"regions.":[114,177],"applies":[117],"probability":[119],"peak":[120],"method":[122],"based":[123],"on":[124],"hierarchical":[126],"analysis":[127],"energy":[130],"barriers":[131],"in":[132],"Poland-Scheraga":[134],"model.":[135],"CONCLUSION:":[136],"Exact":[137],"fast":[139],"computation":[140],"genomic":[142],"profiles":[144],"thus":[146],"feasible.":[147],"Sequences":[148],"several":[150],"megabases":[151],"computed,":[154],"only":[155],"limited":[156],"by":[157],"computer":[158],"memory.":[159],"Possible":[160],"applications":[161],"are":[162],"comparisons":[165],"with":[168],"promotors,":[169],"TSS,":[170],"viral":[171],"integration":[172],"sites,":[173],"other":[175],"melting-related":[176]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2016-06-24T00:00:00"}
